You apply your uniq function when your for loop already is working on the array containing duplicates.

sub uniq {
    my %seen;
    grep !$seen{$_}++, @_;
}

my @filtered = uniq(@lists);
for my $list (@filtered) {
    printGroups($list->{groups}, %group);
    print $list->{line};
    print "\n";
}
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This makes a little more sense, but your uniq function is not doing what you think. It would work if @lists contained scalars, but it doesn't. You need to modify the hash key to produce a scalar value. This will be determined by what constitutes a duplicate. Is it the lines are the same? Or is it based on how many values are in groups? Or what values are in groups? If the first, you want $_->{line} instead of $_.